It's against their rules, they're free to remove it. forget, they're free to remove it regardless. Acting like it's a big deal is 'loving handicapped'.
They removed the sub because it's a loving headache of moderation and it was easier to remove it and deal with the tiny fallout than let a bunch of mouth-breathing chimps napalm everything to solve their stupid conspiracy theory meme. Goddamn.
Against the rule of witchhunting? The sub was focused on the people in the ring itself or various related rings in the past (such as the Franklin case or the UK ring). The Podestas, Alefantis, and the Clintons may be a large part of it, but that's because its an investigation of what they may have done, so of loving course its going to include them. The argument that it's witchhunting is invalid because that's what every investigation is, searching through evidence related to certain people. Besides that, its using public information, so not like its a dox.
"Free to remove it regardless" is a bit of a stretch.

Just because I disagree with something doesn't mean I can delete it.
There is no "tiny fallout", the entire subreddit of r/The_Donald is against them now and the story of u/spez editing comments is now at the front of the site. They're right when they say that some credibility of Reddit is out the window now that its known the admins can shadow-edit any post to say whatever they want.
What if the posts on r/pizzagate were edited? There were already hoaxes and troll accounts trying to disjoint the investigation efforts and stuff the sub up, plus there was uproar in the community itself about how the mods of the sub might be censoring information. Seems like a perfect time to change stuff you don't like and use it as an excuse to delete the sub. Keep in mind that this all comes merely days after the same thing happens on twitter.
So yes, its kind of a big deal. If that makes us 'loving handicapped', so be it.